tbuckley/cabot-search huggingface dataset:
Association of Sodium–Glucose Cotransporter 2 Inhibitors With Time to Dementia: A Population-Based Cohort Study
Authors: Che-Yuan Wu, Carina Iskander, Christa Wang, Lisa Y. Xiong, Baiju R. Shah, Jodi D. Edwards, Moira K. Kapral, Nathan Herrmann, Krista L. Lanctôt, Mario Masellis, Richard H. Swartz, Hugo Cogo-Moreira, Bradley J. MacIntosh, Jennifer S. Rabin, Sandra E. Black, Refik Saskin, Walter Swardfager
Journal: Diabetes Care (2022)

OBJECTIVE Type 2 diabetes (T2D) increases dementia risk, but clear evidence to recommend interventions that can mitigate that risk remains lacking. This population-based retrospective cohort study aimed to determine whether new use of sodium–glucose cotransporter 2 (SGLT2) inhibitors compared with dipeptidyl peptidase 4 (DPP-4) inhibitors was associated with lower dementia risk. RESEARCH DESIGN AND METHODS Ontario residents aged ≥66 years who were new users of an SGLT2 inhibitor or a DPP-4 inhibitor from 1 July 2016 to 31 March 2021 entered the cohort. Incident dementia was identified using a validated algorithm for Alzheimer’s disease and related dementias. Propensity score–weighted Cox proportional hazards models were used to obtain adjusted hazard ratios (aHR) and CIs for time to incident dementia. To address reverse causality and disease latency, the observation window started at 1-year lag time from cohort entry. The primary analysis followed intention-to-treat exposure definition, and a secondary as-treated analysis was performed. RESULTS Among 106,903 individuals, SGLT2 inhibitors compared with DPP-4 inhibitors were associated with lower risk of dementia (14.2/1,000 person-years; aHR 0.80 [95% CI 0.71–0.89]) over a mean follow-up of 2.80 years from cohort entry. When stratified by different SGLT2 inhibitors, dapagliflozin exhibited the lowest risk (aHR 0.67 [95% CI 0.53–0.84]), followed by empagliflozin (aHR 0.78 [95% CI 0.69–0.89]), whereas canagliflozin showed no association (aHR 0.96 [95% CI 0.80–1.16]). The as-treated analysis observed a larger association (aHR 0.66 [95% CI 0.57–0.76]) than the intention-to-treat analysis. CONCLUSIONS SGLT2 inhibitors showed an association with lower dementia risk in older people with T2D. Randomized controlled trials are warranted.
Epidemiology of herpes simplex virus type 2 in Europe: systematic review, meta-analyses, and meta-regressions
Authors: Asalah Alareeki, Aisha M.M. Osman, Mohannad N. Khandakji, Katharine J. Looker, Manale Harfouche, Laith J. Abu-Raddad
Journal: The Lancet Regional Health - Europe (2022)

Herpes simplex virus type 2 (HSV-2) infection is a globally prevalent, life-long, sexually transmitted infection. This study characterized HSV-2 seroprevalence in Europe for various at-risk populations and proportions of HSV-2 detection in genital ulcer disease (GUD) and in genital herpes. Data on neonatal herpes and HSV-2's contribution to HIV transmission were also reviewed.Cochrane and PRISMA guidelines were followed to systematically review, synthesize, and report HSV-2 related findings. The search was conducted in PubMed and Embase databases up to February 20, 2022. Any publication reporting data on the outcome measures was included. Meta-analyses and meta-regressions were conducted.211 relevant reports were identified, including 12 overall incidence measures, 294 overall (813 stratified by factors such as age and sex) seroprevalence measures, 13 overall (15 stratified by sex) proportions of HSV-2 detection in clinically diagnosed GUD, and 70 overall (183 stratified by factors such as age and sex) proportions of HSV-2 detection in laboratory-confirmed genital herpes. Pooled mean seroprevalence was 12.4% (95% CI: 11.5-13.3%) among general populations, 27.8% (95% CI: 17.5-39.4%) among men who have sex with men, 46.0% (95% CI: 40.1-51.8%) among people living with HIV and people in HIV discordant couples, and 63.2% (95% CI: 55.5-70.6%) among female sex workers. Most measures showed heterogeneity in HSV-2 seroprevalence. The pooled mean seroprevalence among general populations increased with age and was 0.65-fold (95% CI: 0.58-0.74) lower in men than women. Seroprevalence decreased by 1% per calendar year. Pooled mean proportions of HSV-2 detection in GUD and in genital herpes were 22.0% (95% CI: 15.3-29.6%) and 66.0% (95% CI: 62.9-69.1%), respectively. HSV-2 detection in genital herpes cases was 1.21-fold (95% CI: 1.10-1.32) higher in men compared to women and decreased by 1% per calendar year. Incidence of neonatal herpes indicated an increasing trend.Although seroprevalence is declining, a significant proportion of Europe's population is infected with HSV-2. HSV-2 accounts for approximately one-fifth of GUD cases and two-thirds of genital herpes cases. Findings support the need to invest in HSV-2 vaccine development, and sexual and reproductive health services.Qatar National Research Fund [NPRP 9-040-3-008] and pilot funding from the Biomedical Research Program at Weill Cornell Medicine in Qatar supported this study.
Pharmacological Targeting of Mitochondria in Diabetic Kidney Disease
Authors: Kristan H. Cleveland, Rick G. Schnellmann
Journal: Pharmacological Reviews (2022)

Diabetic kidney disease (DKD) is the leading cause of end-stage renal disease (ESRD) in the United States and many other countries. DKD occurs through a variety of pathogenic processes that are in part driven by hyperglycemia and glomerular hypertension, leading to gradual loss of kidney function and eventually progressing to ESRD. In type 2 diabetes, chronic hyperglycemia and glomerular hyperfiltration leads to glomerular and proximal tubular dysfunction. Simultaneously, mitochondrial dysfunction occurs in the early stages of hyperglycemia and has been identified as a key event in the development of DKD. Clinical management for DKD relies primarily on blood pressure and glycemic control through the use of numerous therapeutics that slow disease progression. Because mitochondrial function is key for renal health over time, therapeutics that improve mitochondrial function could be of value in different renal diseases. Increasing evidence supports the idea that targeting aspects of mitochondrial dysfunction, such as mitochondrial biogenesis and dynamics, restores mitochondrial function and improves renal function in DKD. We will review mitochondrial function in DKD and the effects of current and experimental therapeutics on mitochondrial biogenesis and homeostasis in DKD over time. <h3>Significance Statement</h3> Diabetic kidney disease (DKD) affects 20% to 40% of patients with diabetes and has limited treatment options. Mitochondrial dysfunction has been identified as a key event in the progression of DKD, and pharmacologically restoring mitochondrial function in the early stages of DKD may be a potential therapeutic strategy in preventing disease progression.
Sex/Gender Differences in the Time-Course for the Development of Substance Use Disorder: A Focus on the Telescoping Effect
Authors: Eleanor Blair Towers, Ivy L. Williams, Emaan I. Qillawala, Emilie F. Rissman, Wendy J. Lynch
Journal: Pharmacological Reviews (2022)

Sex/gender effects have been demonstrated for multiple aspects of addiction, with one of the most commonly cited examples being the "telescoping effect" where women meet criteria and/or seek treatment of substance use disorder (SUD) after fewer years of drug use as compared with men. This phenomenon has been reported for multiple drug classes including opioids, psychostimulants, alcohol, and cannabis, as well as nonpharmacological addictions, such as gambling. However, there are some inconsistent reports that show either no difference between men and women or opposite effects and a faster course to addiction in men than women. Thus, the goals of this review are to evaluate evidence for and against the telescoping effect in women and to determine the conditions/populations for which the telescoping effect is most relevant. We also discuss evidence from preclinical studies, which strongly support the validity of the telescoping effect and show that female animals develop addiction-like features (e.g., compulsive drug use, an enhanced motivation for the drug, and enhanced drug-craving/vulnerability to relapse) more readily than male animals. We also discuss biologic factors that may contribute to the telescoping effect, such as ovarian hormones, and its neurobiological basis focusing on the mesolimbic dopamine reward pathway and the corticomesolimbic glutamatergic pathway considering the critical roles these pathways play in the rewarding/reinforcing effects of addictive drugs and SUD. We conclude with future research directions, including intervention strategies to prevent the development of SUD in women. <h3>Significance Statement</h3> One of the most widely cited gender/sex differences in substance use disorder (SUD) is the "telescoping effect," which reflects an accelerated course in women versus men for the development and/or seeking treatment for SUD. This review evaluates evidence for and against a telescoping effect drawing upon data from both clinical and preclinical studies. We also discuss the contribution of biological factors and underlying neurobiological mechanisms and highlight potential targets to prevent the development of SUD in women.
Global, regional, and national burden of motor neuron diseases 1990–2016: a systematic analysis for the Global Burden of Disease Study 2016
Authors: Giancarlo Logroscino, Marco Piccininni, Benoît Marin, Emma Nichols, Foad Abd-Allah, Ahmed Abdelalim, Fares Alahdab, Solomon Weldegebreal Asgedom, Ashish Awasthi, Yazan Chaiah, Ahmad Daryani, Huyen Phuc Do, Manisha Dubey, Alexis Elbaz, Sharareh Eskandarieh, Farzaneh Farhadi, Farshad Farzadfar, Seyed-Mohammad Fereshtehnejad, Eduarda Fernandes, Irina Filip, Kyle J. Foreman, Abadi Kahsu Gebre, Elena V. Gnedovskaya, Samer Hamidi, Simon I. Hay, Seyed Sina Naghibi Irvani, John S. Ji, Amir Kasaeian, Yun Jin Kim, Lorenzo Giovanni Mantovani, Tivani Phosa Mashamba-Thompson, Man Mohan Mehndiratta, Ali H. Mokdad, Gabriele Nagel, Trang Huyen Nguyen, Molly R Nixon, Andrew T Olagunju, Mayowa Ojo Owolabi, Michael A Piradov, Mostafa Qorbani, Amir Radfar, Robert C Reiner, Mohammad Ali Sahraian, Shahabeddin Sarvi, Mehdi Sharif, Omar Temsah, Bach Xuan Tran, Nu Thi Truong, Narayanaswamy Venketasubramanian, Andrea Sylvia Winkler, Ebrahim M Yimer, Valery L. Feigin, Theo Vos, Christopher J L Murray
Journal: The Lancet Neurology (2018)

Understanding how prevalence, incidence, and mortality of motor neuron diseases change over time and by location is crucial for understanding the causes of these disorders and for health-care planning. Our aim was to produce estimates of incidence, prevalence, and disability-adjusted life-years (DALYs) for motor neuron diseases for 195 countries and territories from 1990 to 2016 as part of the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2016.
Abstract B013: Suppression of TET1 expression down-regulates p16 and contributes to the resistance of SWI/SNF LOF tumors to PRC2 inhibition
Authors: Hailong Zhang
Journal: Cancer Research (2022)

Abstract Polycomb repressive complex 2 (PRC2) drives the expansion of H3K27me3 epigenetic marker and suppress the expression of target genes including tumor suppressors. Activation mutations of EZH2, the catalytic subunit of the PRC2 complex, are thought to be the driver for certain malignancies such as diffused large B cell lymphoma (DLBCL). The SWI/SNF complex remodels nucleosomes to modulate transcription, they are generally considered as tumor suppressors and loss-of-function (LOF) mutations are frequently found across a wide variety of cancers. Many studies suggest that PRC2 is important for the proliferation of tumor cells with SWI/SNF LOF mutations, indeed, EZH2 inhibitor tazemetostat was approved by FDA for epithelioid sarcoma with SWI/SNF subunit SMARCB1 deletion. While not all SWI/SNF LOF tumors respond to PRC2 inhibition, we would like to know what subset of these tumors are sensitive to PRC2 inhibition. In this study, we have developed a potent and selective PRC2 inhibitor BR1763 which blocks the interaction of EED with tri-methylated histone H3 at Lys 27 (H3K27me3) and inhibits cellular H3K27me3 levels. By analyzing the gene expression patterns of BR1763 treated cells, we found that up-regulation of CDKN2A/p16 and down-regulation of E2F downstream gene are essential for cellular response to PRC2 inhibition. Further studies also confirmed that PRC2 inhibition caused P16 up-regulation and induced cell senescence for the sensitive cells. Importantly, suppression of TET1 expression contributes to the resistance to PRC2 inhibition in SWI/SNF LOF tumors, which may be caused by PcG hypermethylation on p16 promoters. TET1 expression, together with SWI/SNF LOF mutation status, can largely predict the sensitivity of tumor cells to PRC2 inhibition. Citation Format: Hailong Zhang. Suppression of TET1 expression down-regulates p16 and contributes to the resistance of SWI/SNF LOF tumors to PRC2 inhibition. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr B013.
Abstract B015: Versatile biochemical and genomic platforms for drug discovery in chromatin remodeling research
Authors: Natalia L. Husby, Lu Sun, Hannah Willis, Matthew R. Marunde, Matt J. Meiners, Zachary Gillespie, Rachel Watson, Saarang Gopinath, Jonathan M. Burg, Marcus A. Cheek, Katherine Novitzky, Bryan J. Venters, Zu-Wen Sun, Michael-Christopher Keogh
Journal: Cancer Research (2022)

Abstract Chromatin remodeling, driven by ATP-dependent remodeling enzymes, plays key roles in regulating gene expression, genome replication and repair. Aberrant nucleosome organization can severely disrupt these important processes, driving various cancers and developmental disorders. Remarkably, nearly 20% of all human cancers contain mutations in subunits from the SWI/SNF family of chromatin remodeling complexes, making them attractive therapeutic targets and interests of basic research. However, studies on the remodeling enzymes (and their multi-subunit complexes) in vitro are challenging partially due to the requirement for nucleosome-based substrates. We have created the EpiDyne® nucleosome remodeling substrate portfolio for use in biochemical assays to examine nucleosome immobilizing activities of chromatin remodelers. Here we present the development of multiple remodeling assays on the EpiDyne® platform (EpiDyne®-FRET, EpiDyne®-PicoGreenTM and EpiDyne®-TR-FRET). These nonradioactive plate-based assays are easy to use, ready for high-throughput inhibitor screening, and can be customized for various remodeling enzymes that exhibit distinct preferences in nucleosome compositions. Furthermore, genome-wide mapping of chromatin remodelers is fundamental for understanding their functions in diseases and responses to inhibitors in cells, but is often obscured by unreliable ChIP-seq approaches. To this end, we have optimized the CUTANA™ CUT&amp;RUN approach to efficiently capture localizations of all major classes of chromatin remodelers with high signal to background. As a complementary research tool to the EpiDyne® platform, CUT&amp;RUN facilitates the epigenomic research on chromatin remodelers for drug discoveries. Citation Format: Natalia L. Husby, Lu Sun, Hannah Willis, Matthew R. Marunde, Matt J. Meiners, Zachary Gillespie, Rachel Watson, Saarang Gopinath, Jonathan M. Burg, Marcus A. Cheek, Katherine Novitzky, Bryan J. Venters, Zu-Wen Sun, Michael-Christopher Keogh. Versatile biochemical and genomic platforms for drug discovery in chromatin remodeling research. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr B015.
Abstract IA006: Systematic functional screening of chromatin factors identifies strong lineage and disease dependencies in normal and malignant haematopoiesis
Authors: Brian Huntly
Journal: Cancer Research (2022)

Abstract Interactions between transcription factors (TF) and chromatin factors (CF) regulate gene expression programmes to determine cellular fate. However, unlike for TF, the exact role of CF in this process is poorly understood. Using haematopoiesis as a model system, we address this fundamental question in lineage choice of normal haematopoiesis and the maintenance of acute myeloid leukaemia (AML). To do this, we have functionally characterized the requirement ex vivo of 550 CFs in normal lineage differentiation and further dissected, with single-cell resolution, the roles of 40 CFs during in vivo lineage commitment (using Perturb-seq). Further, utilizing epigenetic profiling (ATAC-seq and ChIP-seq) we have probed TF-CF interactions that have lineage regulatory potential. Finally, we compare the functions of key CFs and their TF-associations between normal and malignant haematopoiesis. These studies demonstrate, both ex vivo and in vivo, that similar complexes, including three MLL-H3K4 COMPASS methyltransferases (KMTs) and non-canonical (nc-BAF) and canonical BAF (c-BAF) complexes, regulate disparate lineage decisions across haematopoiesis. However, somewhat paradoxically, we demonstrate that unrelated Repressive complexes function similarly, but non-redundantly, to restrain excessive myeloid differentiation and protect lineage diversity. We identify interactions between CF and TF that explain the regulatory function of CF and demonstrate that KO of the nc-BAF member Brd9 leads to a premalignant accumulation of myeloid progenitors, related to impaired recruitment of late myeloid TFs. Finally, utilizing similar experiments in a relevant murine AML model, we identify perturbations of MLL-, BAF- and Repressive CF that trigger partial differentiation and loss of leukaemia potential. Our data also highlight opposing functions for the same CF in normal and malignant haematopoiesis. CFs such as COMPASS members and cBAF remodelers are critical for the balanced differentiation of specific normal haematopoietic lineages, however the same CF are critical for the maintenance of leukaemia fitness, where they act predominantly to maintain differentiation blockade. Finally, we demonstrate that this altered effect occurs through the differential utilization of TF by CF complexes between normal and malignant haematopoiesis, such as corrupted Stat5a-CF interactions, potentially identifying specific CF-TF complexes as therapeutic targets in AML. Taken all together, our work greatly elucidates the role of CF and their TF partners across normal and malignant haematopoiesis. Citation Format: Brian Huntly. Systematic functional screening of chromatin factors identifies strong lineage and disease dependencies in normal and malignant haematopoiesis. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr IA006.
Abstract IA011: Transcriptional dependencies of tuft cell lung tumors
Authors: Christopher R. Vakoc
Journal: Cancer Research (2022)

Abstract Using genetic screens performed in cancer cell lines, we previously identified a tuft cell variant of small cell lung cancer. This novel tumor entity is characterized by high expression of, and addiction to, POU2F3, which encodes a POU homeodomain transcription factor. Subsequent work by several laboratories has revealed tuft cell tumors exist in several different anatomical sites (e.g., thymus, prostate, GI tract), indicating a broader relevance of this cell lineage in human cancer. In my presentation, I will present our efforts to reveal transcriptional mechanisms in tuft cell lung tumors, focusing on the identification of OCA-T1 and OCA-T2 as coactivators of POU2F3. Citation Format: Christopher R. Vakoc. Transcriptional dependencies of tuft cell lung tumors. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr IA011.
Abstract A030: Deciphering the micro-RNA landscape of AKT isoforms and its clinical impact in patients with lung adenocarcinoma
Authors: George Laliotis, Pauline Lin
Journal: Cancer Research (2022)

Abstract Over the last 25 years, AKT kinase has been thoroughly investigated and characterized as a crucial regulator of cellular homeostasis, affecting a plethora of essential molecular functions. The three identified isoforms of this kinase, namely AKT1, AKT2 and AKT3, often display opposing and antagonizing cellular functions. One of these important cellular functions is the expression and activation of micro-RNAs (miRNAs), an important RNA process that epigenetically regulates the human transcriptome. In the context of human cancer and based on several reports, AKT kinase has been associated with aberrant expression of oncogenic miRNAs, that in turn hijack oncogenic pathways, leading to tumor progression, metastasis and resistance to therapy, especially in lung adenocarcinoma (LUAD). Nevertheless, a comprehensive analysis of the impact of each AKT isoform on the regulation and enrichment of a specific miRNA signature in lung adenocarcinoma has yet to be performed. Here, we were willing to elucidate the miRNA epigenetic landscape and downstream targets, driven by each AKT isoform, and its clinical importance in patients with lung adenocarcinoma. To this extent, we utilized RNA-Seq and Small RNA-Seq data from The Cancer Genome Atlas (TCGA-LUAD) to identify the miRNA signatures related with the expression of each AKT isoform in LUAD. Gene Set Enrichment Analysis from RNA-Seq and miRNA levels analysis from Small RNA-Seq, identified a unique miRNA signature for each AKT isoform, demonstrating their largely opposing effect in miRNA profiling. In parallel analysis, in silico target analysis of the top 50 regulated miRNAs, demonstrated another set of unique targets for each isoform-dependent miRNA signature, which is involved in metabolism, DNA damage, RNA processing, cell survival, immune response and metastasis. More importantly, clinical and survival analysis revealed that the top 50 Differentially regulated miRNAs, ranked by q-value, for each isoform correlated with poor progression free survival in patients with LUAD. Collectively, our atlas of AKT isoform-driven miRNA landscapes implicates AKT as a global effector of miRNA landscape in lung adenocarcinoma. Due to the lack of reliable isoform-specific AKT inhibitors, the identification of the oncogenic miRNA networks regulated by each isoform, acts as an important transnational resource for the design and testing of inhibitors that bypass AKT inhibition toxicity, sparing its impactful physiological functions. Citation Format: George Laliotis, Pauline Lin. Deciphering the micro-RNA landscape of AKT isoforms and its clinical impact in patients with lung adenocarcinoma. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr A030.